Microbiology Commons^™

Reversible Degradation Of Peptidoglycan By Lytic Transglycosylases, Aaron Devereaux

Theses and Dissertations (Comprehensive)

Antimicrobial resistance continues to be a burden on the global healthcare system with an estimated cost of billions of dollars and millions of deaths each year. Recently, there has been little to no development on new antibiotics to treat bacterial infection, and any that are developed become resisted to within a few years. Both Gram-positive and Gram-negative bacteria contain a mesh-like layer called peptidoglycan (PG) that surrounds their cells providing strength, cell shape, and protection from their environments. This layer is a polymer of N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) connected via a b-1,4-glycosidic bond, with each strand being cross-linked …

Cultures For Acid-Fast Bacilli: Are We Being Good Stewards?, Jennifer Hanrahan, Julie D. Sill, Patricia Ver Schneider, Jessica F. Copeland, Elsie Frimpongmaa Amoako-Kissi, Ogochukwu O. Ilobi, Angela J. Toepp

Department of Medicine Faculty Publications

Objective: To describe the use of cultures for acid-fast bacilli (AFB) and situations in which AFB cultures are unlikely to be of clinical benefit.

Design: Retrospective descriptive study of AFB cultures submitted to Sentara Health microbiology laboratory from December 1, 2021, to December 1, 2023. Data were collected from the electronic medical record and included patient demographics, the service line that ordered the culture, specimen source, and culture results.

Setting: Sentara Healthcare System.

Patients: All patients who had specimens submitted to the microbiology laboratory during the study period were included.

Results: A total of 13,944 AFB cultures from 8,243 …

Oral Microbiome And Inflammatory Bowel Disease: New Understanding And Call To Action, Michael Saadeh, Sydney Donohue, Shaina Ailawadi, Gordon Hong, David A. Johnson

Department of Medicine Faculty Publications

The oral microbiome is the second largest microbial community in the human body after the gut microbiome. It includes an array of fungi, bacteria, amoebae, flagellates, archaea, and viruses, all of which are potential pathogens. This microbiome can act as a facilitator not only for protection but also for aggravation when dysbiosis occurs. Although conventional thought is this is primarily in terms of oral health issues, such as dental caries and gingival disease. The systemic effects of the oral microbiome however, are relevant to both gastrointestinal (GI) disease and non-GI disease. These systemic risks occur for several reasons, including upregulation …

Practical Experimental Microbiology: Laboratory Manual, Rivka Levron

Open Touro Created

2025

Microbiology, especially the laboratory component, is a highly practical and useful course for students pursuing many career options. While a number of excellent microbiology laboratory manuals are available, many are more suitable for a full-year course in microbiology or for more advanced studies.

Microbiology Experimental Laboratory Manual is comprehensive in teaching students basic microbiological techniques, i.e., how to grow and stain bacteria, how to identify bacteria and fungi, and means of identifying different species of bacteria microscopically. Further experiments enable students to identify the most effective soap/detergent from those readily available; to discover which spices have the most anti-bacterial …

Cath-Ddg: Towards Robust Mutation Effect Prediction On Protein-Protein Interactions Out Of Cath Homologous Superfamily, Guanglei Yu, Xuehua Bi, Teng Ma, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic studies. Recently, deep learning models using protein 3D structures have become predominant for predicting mutation effects. However, significant challenges remain in practical applications, in part due to the considerable disparity in generalization capabilities between easy and hard mutations. Specifically, a hard mutation is defined as one with its maximum TM-score < 0.6 when compared to the training set. Additionally, compared to physics-based approaches, deep learning models may overestimate performance due to potential data leakage.

Results: We propose new training/test splits that mitigate data leakage according to the CATH homologous superfamily. Under the constraints of physical …

Engineering Extracellular Vesicles (Evs) To Combat Infection And Inflammation In Cystic Fibrosis, Sharanya Sarkar

Dartmouth College Ph.D Dissertations

Cystic Fibrosis (CF) is a multisystemic genetic disorder caused by mutations in the CFTR gene, resulting in chronic pulmonary infections, hyperinflammation, and progressive lung damage. Among the pathogens that colonize CF lungs, Pseudomonas aeruginosa (P. aeruginosa) is predominant, infecting over 50% of adults with CF and developing antibiotic resistance over time. Current modulator therapies fail to address persistent bacterial infections, chronic inflammation, or irreversible lung damage, underscoring the need for novel therapeutic strategies. In our previous in vitro studies, we demonstrated that extracellular vesicles (EVs) secreted by primary Human Bronchial Epithelial Cells (HBECs) inhibit P. aeruginosa growth by reducing the …

Biochemical And Molecular Analysis Of Anr-Dependent Microoxic Fitness Factors In Pseudomonas Aeruginosa, Stacie E. Balsam

Dartmouth College Ph.D Dissertations

Pseudomonas aeruginosa is a prominent opportunistic pathogen that is often found in microoxic environments like sites of infection and colony biofilms. P. aeruginosa can grow at oxygen (O2) at concentrations as little as 3 μM and also grows anaerobically by generating energy using nitrate as an alternate electron acceptor. An important way P. aeruginosa adapts to low O2 is through Anr, a transcription factor that upregulates many genes important for microoxic and anoxic fitness.

Specifically, Anr regulates mhr which encodes a hemerythrin protein (Mhr) that binds O2 with affinities relevant to microoxia and is also necessary for full fitness of …

A Novel Silver-Ruthenium-Based Antimicrobial Kills Gram-Negative Bacteria Through Oxidative Stress-Induced Macromolecular Damage, Patrick O. Tawiah

Theses and Dissertations

The rise in drug-resistant bacteria, together with the decline in antibiotic development, requires new strategies for infectious disease control. Gram-negative pathogens are particularly challenging to combat due to their outer membrane. This study highlights the effectiveness of the silver-containing antimicrobial AGXX® against the Gram-negative bacterium Escherichia coli. AGXX® is a promising silver coating that presumably kills bacteria through the generation of reactive oxygen species (ROS). However, neither AGXX®’s mode of action is fully understood, nor have its effects on Gram-negative bacteria or bacterial response and defense mechanisms towards AGXX® been studied in detail. Here, I report that the bactericidal …

The Formation And Degradation Of Carboxysomes During Heterocyst Development In Filamentous Cyanobacteria, Maxwell Anton Jakubiak

Electronic Theses and Dissertations

Photosynthetic carbon (CO2) fixation and solar-powered nitrogen (N2) fixation are foundational biochemical processes that introduce essential elements into the biosphere. While atmospheric dinitrogen gas (N2) is unusable to most organisms, diazotrophs utilize the nitrogenase enzyme to reduce N2 to ammonia. Because all known nitrogenases are highly susceptible to irreversible oxygen inactivation, N2 fixation is generally incompatible with oxygenic photosynthesis. However, several cyanobacteria are both photosynthetic and diazotrophic, balancing these opposing metabolisms by temporally or spatially separating the respective enzymes. Anabaena sp. PCC 7120 is a model multicellular cyanobacterium that grows in filaments of photosynthetic vegetative cells, which respond to nitrogen …

Isolation, Characterization & Identification Of Cultivable Field Pea Seed Bacteria In South Dakota, Diana Wairimu Njuguna

Electronic Theses and Dissertations

Pea (Pisum sativum L.) is a legume, cultivated on over 25 million acres, particularly in Canada, France, China, Russia, and the United States. Its seeds harbor microbiota including bacteria and fungi, either on the surface (epiphytes) or within seed tissues (endophytes). These microbes can be pathogenic or beneficial, enhancing seedling metabolism and protection from environmental stresses. Characterizing beneficial seed microbiota enables development of microbial inoculants for seed treatment. Seeds from 12 varieties (green or yellow seed coats) were harvested from Sturgis and Dakota Lakes in 2021. Epiphytes were extracted using sonication followed by grinding the seeds to obtain endophytes. Isolates …

Interactions Between Lipopolysaccharide And Capsule Retention In Klebsiella Pneumoniae And The Resultant Effects On Macrophages, Juliane Leigh Nguy

UNF Graduate Theses and Dissertations

Klebsiella pneumoniae is the third most common cause of nosocomial infections in the United States. The capsular polysaccharides (CPS) are virulence factors allowing K. pneumoniae to evade host immune systems. The current model of capsule structure indicates that CPS fibrils interact with the external O-antigen of lipopolysaccharide molecules to enhance retention to the bacterial outer membrane. These interactions may influence pathogenicity in clinically relevant strains. This study characterized alterations to LPS and CPS structure, the impact of these changes on capsule retention, membrane permeability, biofilm formation, and macrophage interactions. LPS and CPS were quantified and visualized in four strains of …

Microbial Hydrocarbon Degradation And Carbon Cycling In Marine And Freshwater Sediments: A Comparative Metagenomic Analysis, Yogita M. Warkhade

Dissertations, Master's Theses and Master's Reports

Microbes are essential in keeping our environment balanced, especially by fixing carbon dioxide and breaking down hydrocarbons in aquatic sediments. This thesis explores how microbial communities perform these tasks in different sediment environments, including marine areas (Caspian Sea and Mediterranean Sea) and freshwater ecosystems (Great Lakes). The first part of this thesis reviews current knowledge about how microbes degrade hydrocarbons. It highlights the importance of different pathways microbes use depending on oxygen availability. The second part provides a detailed study of the microbial communities found in marine sediments from the Caspian Sea and Mediterranean Sea, showing that microbes in these …

The Impact Staphylococcus Aureus Has On Conventional And Organic Dairy Herds In New Hampshire And New York, Jacqueline Rose Holmes

Honors Theses and Capstones

Staphylococcus aureus is a potentially virulent bacterium that causes mastitis in dairy cattle. The toxins produced from S. aureus impact host immunity, damage the mammary gland, and can adapt to cause antimicrobial resistance. It is important to manage both organic and conventional farms correctly by practicing proper hygiene while milking and providing a clean environment. There is a significant increase of S. aureus cases on organic farms compared to conventional, so there may be ways in which organic management and treatment options could be altered to reduce economic loss and animal suffering. The thesis focuses on the involvement S. aureus …

Investigating The Dna-Binding Role Of Tbp1 In Toxoplasma Gondii: Expression And Characterization Of A Recombinant Protein, Madison T. Jeckell

Honors Theses and Capstones

Toxoplasma gondii is an obligate intracellular parasite with a complex life cycle and an unusual transcriptional machinery compared to other eukaryotes. Unlike most organisms, Toxoplasma lacks multiple well-conserved promoter motifs and has multiple TATA-binding proteins (TBPs), including TBP1, whose function in DNA binding and transcription regulation is poorly understood. This study aimed to generate and express a recombinant TBP1 protein from Toxoplasma to enable future DNA-binding assays and motif identification. Using RT-PCR, the TgTBP1 gene was amplified and cloned into a pGEX vector to produce a GST-tagged protein. The recombinant plasmid was transformed into E. coli BL21 cells, and protein …

Backyard Chimeric Microbiomes: K-12 Participatory Science, Abigail Saucier

Honors Theses and Capstones

The US education system has seen a recent push for more secondary school curriculum to include STEM (Science, Technology, Engineering, and Mathematics) materials and activities. Middle and high school is a pivotal time when academic and personal experiences affect the development of student attitudes towards STEM (Christensen et al., 2015; Moreno et al., 2016). Teachers often utilize hands-on activities to promote student engagement with science curriculum (Brooks & Poles, 2021; Christensen et al., 2015). Hands-on activities improve student learning, but impacts vary by type of activity. When students work towards a known outcome they can feel disconnected from the work …

The Influence Of Flower-Microbe Interactions On Bumble Bee Behavior And Gut Microbiome Composition, Success Chiamaka Ekemezie

Graduate Theses/Dissertations

This thesis examines how microbial interactions in floral nectar and environmental variation influence bumble bee (Bombus spp.) foraging behavior and gut microbiome composition. Pollen germination experiments and behavioral assays in the lab tested whether Metschnikowia reukaufii (yeast) and Acinetobacter nectaris (bacteria) induce pollen germination and bursting in nectar and affect bee behavior subsequently. Both microbes reduced intact pollen, but bees did not alter flower preference. Furthermore, the study also assessed how floral and bee community composition shaped gut microbiome composition across six Missouri prairies. Using amplicon-sequenced fungal ITS and bacterial 16S rRNA genes, I found that fungal microbiome composition varied …

Genomic And Metabolic Network Properties In Thermophiles And Psychrophiles Compared To Mesophiles, Amal Saeed Alblooshi

Theses

Thermophiles and psychrophiles are extremophilic microorganisms that thrive in harsh conditions. Thermophiles are mostly located in hot springs, prosper in high temperatures. Psychrophiles thrive in extremely cold environments, including polar regions and deep-sea habitats. Although they play a crucial role in biotechnology and environmental research, their mechanisms of adaptation are still not well understood. The main objective of this thesis is to understand the genomic characteristics and metabolic network features in thermophiles and psychrophiles compared to mesophiles. The genomes of 59 species among thermophiles, psychrophiles, and mesophiles were collected from the NCBI database. These genomes were used to analyze their …

Evaluation Of Microbial Contamination In Tube Well And Filter Water Of Lahore And Treatment With Copper Nanoparticles, Khadeeja Moazzam, Sumaira Mazhar

Journal of Bioresource Management

Water contamination is a global issue and different techniques are being devised to reduce water contamination. Among these techniques, use of nanoparticles for water purification is an efficient and cost-effective method with minimum or no side effect. Metal nanoparticles are known for their antibacterial activity against various pathogens. Synthesis of these nanoparticles using green synthesis methods minimizes the harmful effects while ensuring their antibacterial activity. Therefore, in the present work, it was aimed to evaluate the microbial contamination in water samples collected from different tube wells and filter plants located in different areas of Lahore, Pakistan for the isolation of …

Degradation Of Cyanobacteria And Microalgae Using Ultraviolet Radiation At 222 Nm And Its Application In The Bleaching Of Lampenflora On Cave Rock Surfaces, Keisuke Naito, Shuji Watanabe, Masuo Komukai, Takehiro Kazama, Masayuki Itoh, Masahiro Kawasaki

International Journal of Speleology

Cyanobacterial and microalgae blooms negatively affect ecological environments. One of the emerging problems of these blooms occurs in calcareous caves, where visible lighting systems in tourist caves induce the formation of photosynthetic biofilms known as lampenflora on rock surfaces. In this study, we evaluated the inactivation effect of ultraviolet (UV) light irradiation at 222 nm (rare gas halide lamp) and 254 nm (mercury lamp) on cyanobacteria and microalgae in a laboratory and on lampenflora in Ryusenshindo Cave in Japan. Based on the laboratory experiments, irradiation at 222-nm was more effective than that at 254-nm for degrading plants. The photosensitivity of …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …